The hard tissue of the Japanese pearl oyster, Pinctada fucata, consists of two layers, the outer prismatic layer, bearing calcite, and the inner nacreous layer, bearing aragonite. An EDTA-insoluble fraction of the prismatic layer of P. fucata was extracted with urea. In-vitro crystallization experiments showed that this urea-soluble fraction contained the factor(s) that promoted the growth of calcite crystals. We purified a protein from this fraction and deduced the internal amino acid sequences EYDFDRPDPYDP and EYDFERPD. We performed 3′ RACE using primer DPPF1, encoding EYDFDRPDPYDP, and an oligo-dT adapter primer and amplified a fragment of approximately 300 bp. We screened cDNA libraries using the 300 bp fragment and obtained two clones that we named prismin 1 and 2. Both cDNAs encode proteins of 51 amino acids. Homology searches revealed 91% amino acid identity between prismin 1 and 2. The synthetic peptide DFDRPDPYDPYDRFD, corresponding to the carboxy terminal region of prismin 1, has calcite growing activity and calcium binding capability, showing that the carboxy-terminal region is a functional domain. Prismin 1 is expressed strongly in the outer edge and in the inner part of the mantle tissue. However, immunoblot analysis revealed that prismin protein exists only in the prismatic layer, not in the nacreous layer, despite the presence of the mRNA. Therefore, we conclude that prismin is a novel prismatic layer-specific calcite growth factor.